Quality Filtering and Read Mapping
Short-fragment reads, rRNA reads, adapter/ primer and low quality reads were filtered from Fastq files of raw data by using Trimmomatic v 0.35 (Bolger et al. , 2014) and FASTX-toolkit present in the FastQC (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/). High-quality filtered reads were mapped to Glycine max reference genome (G max1.1 version ) available at Phytozome v9.0 database ( Schmutz et al. , 2010; Goodstein et al. , 2012) using HISAT2 software (Kim et al., 2015).